Perhaps a plot twist could be that the time - travel device they use was actually created by an ancient and forgotten wizard who had a hidden agenda. When Hermione and Lucius travel back, they discover that this wizard was trying to use them to change history for his own gain. They then have to race against time (literally) to stop this wizard from achieving his goal while also trying to return to their own time. This would add an extra layer of mystery and danger to their time - traveling escapade.
Often, a plot twist might involve Hermione uncovering a secret that Lucius has been hiding. This could be related to some dark magic he's involved in or a family secret. This discovery could then give Hermione some leverage over Lucius. Or perhaps there's a twist where other characters from the Harry Potter universe get involved. Like Harry and Ron coming to rescue Hermione, but she refuses to leave because she's in the middle of a complex plan to bring down Lucius from the inside.
One idea could be that Hermione, using the Time - Turner, accidentally goes back to a time when Lucius was a young Death Eater in training. She tries to subtly change his path, which leads to a series of events where they form an unlikely alliance. They might start to understand each other's motives and values more deeply.
Perhaps the person who initiates the time travel isn't who they seem. It could be an imposter who has their own motives for changing the past, like a Shadow in disguise. This would add a whole new layer of mystery and danger to the story.
One interesting plot twist could be that Lucius tries to use Hermione as a spy within Dumbledore's Army. He might think that he can manipulate her into getting information for the Death Eaters. But Hermione, being as clever as she is, turns the tables on him and feeds him false information. Another twist could be that Hermione discovers a long - lost family secret that explains how she and Lucius are related and that this secret has the power to either redeem Lucius or completely destroy the Malfoy family name.
One common theme is the clash of values. Hermione, with her modern and inclusive values, often clashes with Lucius's old - fashioned pure - blood ideology. Another theme is the power of knowledge. Hermione's knowledge from the future can be a great advantage or a source of trouble in the past. And of course, there's the theme of love or at least a complex relationship that develops between them despite their initial differences.
Perhaps Draco saves Hermione in a very public and unexpected way. This could lead to a huge scandal in the wizarding world. Lucius might be shamed and lose a lot of his influence among the Death Eaters. Draco, on the other hand, might find himself an outcast among his own family and former friends. Hermione, feeling indebted to Draco, might try to protect him from the backlash, which could further develop their relationship in an interesting way. It could also be that Draco's act of saving Hermione is part of a prophecy that neither of them knew about. This could add a layer of mystery and destiny to their story.
Well, a possible plot twist is that when they travel back in time, Sakura loses her medical skills. This forces her to learn them all over again in a more difficult environment in the past, and in the process, she discovers a new way of using medical ninjutsu that she brings back to the future. As for Kakashi, his Sharingan might behave differently in the past due to some temporal anomaly. This could lead to him having to control a new and unexpected power while also dealing with the enemies from that era. Also, they might find out that their time travel was actually set up by an enemy who wants to use their presence in the past to change the future to their advantage.
One interesting plot twist could be that the Sannin travel back to a time when Orochimaru was still a good - hearted ninja. They could try to prevent his fall to the dark side. This would change the entire future of the Naruto world as Orochimaru's actions had a huge impact on many events.
Perhaps a really cool plot twist is that the time travel was actually a trap set by an old enemy. When Kakashi and Naruto travel back, they find out that this enemy has been manipulating events from the past all along. They then have to not only fix the past but also figure out a way to stop this enemy from using the past to destroy their future.
Well, a cool plot twist could be that Naruto and Mito time travel to a period right before the Nine - Tails was sealed in Mito. Naruto, with his knowledge of the future, tries to find an alternative way to deal with the Nine - Tails' power. This could completely change the history of the Uzumaki clan and the Hidden Leaf. Also, they could time travel to a time when the first Hokage was still alive and Naruto has to convince him of future threats without revealing too much. Or perhaps they travel to a time when a powerful enemy was about to attack the village, and they use their future skills to defeat the enemy in a way that shocks everyone in the past.